I've been a little involved with dogs and dog breeding, so my perspective on animal (insect) breeding tends to come from that back ground. In our area, you typically buy 3 #s of bees with a queen for $85.00 and start from there. Not much thought is given into the "line" of stock. It's either an Italian or Carnie Queen, that is included in the 3 # purchase. Your package of bees comes from California or Texas from a bee packager, who you don't really know or know well.
After reading some of the material posted, it seems that a better approach might be taken in selecting your queen and creating a "foundation" stock. Even, with "natural breeding", some efforts can be made to improve your "line" of bees over time.
After a short search on the net, I found several sources of queens, that are specifically produced for sale to "Queen Breeders". These queens are costly (~$100.00) and advertised as having special traits.
Assuming that you wanted to consider producing your own "line" of queens .... for your own use and environment........ how best to start? (You can always start using the concept of hybrid vigor, if nothing else.)